Getting Started - renaultJB/GIBOC-Knee-Coordinate-System GitHub Wiki

Getting started

This document provide the method to use the associated code to construct anatomical coordinate systems (ACSs) to the knee bones.

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The first thing to know is that the functions to construct ACSs are independent, each algorithm rely only on the information provided by the geometry of the current bone. It is also important to note that the algorithms are independent of imaging coordinate systems as demonstrated in the paper (See also Supplementary Material-C).

To construct an ACS the required input is a .STL or .MSH file with as isotropic as possible triangles of 0.5mm characteristic length. When segmenting medical images the general output is a .STL file, this file can be remeshed to 0.5mm isotropic mesh with different software. We provide a function to do it with GMSH (see How to a Generate Nice Mesh from .STL) but it can also be performed in 3-Matic and certainly be achieved with MeshLab or HyperMesh from Altair.

Once, you have your file you can check the example file (Example.m) and modify it to adapt it to your need to see how to use the functions.

For now the all the algorithm variants are run we the function are called, soon we will implement a way to do allow the user to select the method he wish to use.

If you plan on reading .MSH file generated with GMSH we should link your Matlab software with the Python engine, this is quite easy and well documented here [Not necessary anymore]

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